Biochemistry 1: Amino Acid PDF

Faculty of Physical therapy Biochemistry 1 Amino acid Dr. Esraa M. Elnshar  protein Proteins are Large molecules made up of 20 amino acids linked together in long chains called polypeptides Amino acids are the building blocks for proteins found in all livi...

Faculty of Physical therapy Biochemistry 1 Amino acid Dr. Esraa M. Elnshar  protein Proteins are Large molecules made up of 20 amino acids linked together in long chains called polypeptides Amino acids are the building blocks for proteins found in all living cells.  Amino acid Amino Acids are the building units of proteins. There are about 300 amino acids occur in nature. Only 20 of them enter in proteins synthesis. Amino acid found in cells and in Composition proteins is in the L consists of carboxyl group and basic configuration. amino group bonded to α-carbon (C- atom next to COOH) Side chain (R) bound to a-carbon. R identifies amino acid  Amino acids in protein must be 1. α-amino acid The amino group attached to the next carbon of the carboxyl group is called “α-amino acid”. All naturally occurring amino acids in protein ar “α-amino acids” 2. L-amino acid It can occur in one of the forms: the L-form (left-handed form) 3. amino acids are chiral, α- carbon has 4 different groups attached to it except glycine. Classification of Amino Acids: I. Classification based on Chemical structure [R group] II. polarity III. Nutritional Classification IV. Metabolic Classification Classification according to R-Group Amino acids can be classified into 3 groups : Aliphatic [ R= Carbon Chain, not ring] Aromatic [ Benzene Ring] Heterocyclic amino acids [ Ring with hetero atoms (S,N,O), not contain benzene ring] Aliphatic amino acids 1. Aliphatic neutral amino acids: a) simple: These have no functional group in their side chain [ non branched, (Example: glycine, alanine)] or [branched (ex: valine, leucine, isoleucine)] b) Hydroxy amino acids: These have a hydroxyl group in their side chain. Ex: serine, threonine c) Sulfur containing amino acids: have sulfur in their side chain. Ex: cysteine, methionine 2. Aliphatic acidic amino acids: have carboxyl group in their side chain. Ex: Aspartic and Glutamic acid [COOH > NH2] 3. Aliphatic basic amino acids: contain amino group in their side chain. Ex: Lysine, Arginine [NH2 > COOH] Guanido group Acid amide amino acid Glutamine  Aromatic amino acids have benzene ring in their side chain. Ex: phenylalanine, tyrosine.  Heterocyclic amino acids have a side chain ring which possess at least on atom other than carbon Ex: Tryptophan, histidine, proline. Tryptophan Classification according to polarity of side chain (R) Polar amino acids: in which R contains polar hydrophilic group so can forms hydrogen bond with H2O. R may contain: OH group : as in serine, threonine and tyrosine SH group : as in cysteine amide group: as in glutamine and aspargine NH2 group or nitrogen act as a base (basic amino acids ): as lysine, arginine and histidine COOH group (acidic amino acids): as aspartic and glutamic. Non polar amino acids: R is alkyl hydrophobic group [aliphatic and aromatic group] which can’t enter in hydrogen bond formation. They are embedded in other hydrophobic structures, such as interior of cell membranes. amino acids are non-polar (glycine, alanine, valine, leucine, isoleucine, phenyl alanine, tryptophan, proline and methionine). Classification according to nutritional requirements Essential amino acids:  Non essential amino acids:  Semi-essential amino cannot be synthesized by An amino acid that can be acids: the body. As a result, they made by humans and so is formed in the body but must come from food. Their essential to the human diet. not in sufficient amount deficiency affects growth, The nonessential amino for body requirements health and protein synthesis. acids: Alanine, asparagine, especially in children. The essential amino acids are: aspartic acid, cysteine, Arginine and histidine Arginine, histidine, valine, glutamic acid, glutamine, are semi-essential. isoleucine, leucine, lysine, glycine, proline, serine, and methionine, threonine, tyrosine tryptophan and phenylalanine. Classification according to Metabolic Amino acids can be classified according to their metabolic in the body. They are degraded inside our body by removal of the amino group in the form of ammonia (NH3) and leave the carbon skeleton. Purely ketogenic: These amino acids enter the metabolic pathway of ketone bodies. i.e They can give ketone bodies e.g. Leucine and lysine α-keto acid Purely glucogenic: They can give glucose e.g. glycine, alanine, valine, serine, threonine, cysteine, methionone, aspartic acid, asparagines, glutamic acid, glutamine, arginine, histidine and proline Ketogenic and glucogenic: During metabolism, they can give ketone bodies and glucose e.g. isoleucine, phenylalanine, tyrosine and tryptophan. Physical properties  Colourless  Crystalline in nature  Melting point above 200ᵒC  Soluble in polar solvent and Insoluble in non polar solvent Amino acid can be present in 2 configuration ( L- and D-  All amino acids possess optical isomers except isomers) glycine due to the presence of asymmetric α- L- isomer only present in carbon atoms. protein.  Some are structurally stable and sterically hindered [Glycine]  Amino acids [proteins]posses enzymatic activities  Amino acids exhibit colloidal nature and denaturing property Acid–Base Properties of Amino Acids Although we commonly write amino acids with whole carboxyl group and amino group, their actual structure is ionic and depends on the pH. The carboxyl group loses a proton, giving a carboxylate ion, and the amino group is protonated to an ammonium ion. This structure is called a dipolar ion or a zwitterion (has both +ve and –ve charges (net charge=zero)). Isoelectric Point (PI): The pH at which the amino acid molecule carries no net charge. Because amino acids contain both basic –NH3+ and acidic COO- groups, they are amphoteric (having both acidic and basic properties). In an acidic solution, the -COO- group is protonated to a free –COOH group so the molecule has positive charge. In alkaline solution, -NH3 + loses its proton, the molecule has an overall negative charge. Chemical properties 1) Detection for amino acids (Ninhydrin test) When ninhydrin reacts with an amino acid, one of the products (reduced ninhydrin) is a deep violet. The side chain of the amino acid is lost as an aldehyde. 3) Decarboxylation: The amino acids will undergo decarboxylation to form the corresponding “amines”. Thus amines are produced Histidine → Histamine + CO2 Tyrosine →Tyramine + CO2 Lysine →Cadaverine + CO2 4) Reaction with Alkalis (Salt formation): The carboxyl group of amino acids can release a H+ ion with the formation of Carboxylate (COO–) ions. 5) Reaction with Alcohols (Esterification): the amino acids is reacted with alcohol to form, “Ester”. The esters are volatile in contrast to the form 6) Formation of peptide bonds: Amines and acids can condense, with the loss of water, to form amides. Amino acid has both an amino group and a carboxyl group to form an amide linkage (covalent bond). The amide linkage between the amino acids is called a peptide bond.  Proteins are made of polymerization of amino acid through peptide bonds. 7) Disulfide Linkages Amino acid with SH side chain can form covalent bond. Cysteine can form disulfide bridges (also called disulfide linkages) which can join two chains. Functions of Amino Acids: L-α-amino acids and their derivatives participate in some cellular functions e.g.:  Nerve transmission e.g. glutamate, serotonin & dopamine  Biosynthesis of porphyrins, purines, pyrimidine and urea  Thyroid hormones and adrenaline are synthesized from tyrosine  Some hormones, hormone-releasing factors, neuromodulators, or neurotransmitters are peptides